VisMu

System requirements

VisMu can be executed on any Windows Linux or MacOS X computer with installed Java version 1.4 or higher.
Follow these instructions to install Java on your machine:
Windows | Linux | Solaris

Macintosh users should upgrade their OS to 10.1 or better. Additional java upgrades may be available from Apple's download page.

Installation instructions

download the archive for windows, MacOS X or Linux
Save the file on your desktop
Start the vismu.exe program by clicking on the icon
The program will create a folder Vismu with several files. After this the archive can be removed.
Windows user can run program by executing the start.bat file
Linus and Mac Users must execute the start file
Note for UNIX users: files cluster must be executable.

User manual

Input files

File	status	description
Sequence	mandatory	FASTA format file. Distributive package contains an example file ABO.fsa
Pretty base	mandatory	This text format file contains list of all deviations from original sequence for other samples.See example file for details
annotation	optional	This text format file contains annotation. Each line of the file contains description of one annotated region and starts with three fields separates by space: annotation_type start_pos_on_query end_pos_on_query. Other fields will be ignored. See example file for details
Protein alignment	optional	This FASTA format file contains protein alignment aligned to the main sequence. See example file for details

The distributive package contains some example files. The start.bat will rum VisMu with these input files: -rs=ABO.fsa -an=annot.txt -pb=abobg.prettybase.txt -pa=boproteinalignment.mfa and user can edit the start.bat file by using the right button of the mouse and replace the name of the files by yours. See Usage section for details. If program will found that some mandatory files were omitted it will open a Wizard window so you can open necessary files at program startup.

Wizard window Relation between wizard and command line parameters

Wizard parameter Command line
parameter

Ref. Seq -rs

Annotation -an

Pretty Base -pb

Protein Alignment -pa

Overview of the display

Click on any part of the image to see details

Program Window

Toolbar

Zoom in or zoom out view window

Scroll left or right 1/2 window width from current position

Recalculate tree and rebuild view

Control Panel

Control Panel contains the following elements:

Start: Start position on the gene
End: End position on the gene
Cut Off
Set button: Sets new position on the genome
Clustering method: Allows to select parameters to the cluster program. For details see documentation for the clustering program.
Sorted: This parameter also affect clustering program and influence the order of its output
Distance method: This option changes the way how distance between two samples will be calculated.

Coordinate ruler

The top panel of the program shows annotation in gene coordinates. Semi-transparent red rectangle shows current position relative the whole gene length. You can drag this rectangle by mouse to change current position or drag left or right rectangle borders to change start or end position respectively.

Tree Panel

Tree panel reflects results of clustering procedure. Tree panel is mouse clickable. Each click on small blue rectangles will hide corresponding branch of the tree. Repetitive click in the same rectangle will show hidden branch. After each tree recalculation tree panel will show the whole tree with all branches visible.

Zoom Panel

Zoom panel shows positions of mutation points on the zoomed area of the first sequence and points to their positions on the mutations panel.

Mutation Panel

Protein alignment panel

Status Bar

Status Bar is used to show current status messages and contains progress bar

Usage

java [-Xmx###M] -classpath "... ..." DTree parameters
For classpath details see corresponding starting script.

Parameter Default Comment

-cl ./cluster Path to cluster program

-rs Fasta File

-an Annotation File

-pb Pretty Base File

-ps Protein Alignment File

-d Debug output

Parameter	Default	Comment
-cl	./cluster	Path to cluster program
-rs		Fasta File
-an		Annotation File
-pb		Pretty Base File
-ps		Protein Alignment File
-d		Debug output

Troubleshooting

starting scenario assumes that java executable file is available from the standard path
If it's not so you can either add your java directory to your path or you can edit scenario file (start.bat or start) and replace the "java" by its absolute path
Not enough memory error:
You can increase amount of memory available to Java machine by changing the -Xmx###M parameter.
### must be replaced by amount of memory in megabytes. Edit start or start.bat
file to increase this parameters if default value -Xmx350M is not enough for your data set.

		Zoom in or zoom out view window
		Scroll left or right 1/2 window width from current position
		Recalculate tree and rebuild view